Starting phenix.real_space_refine on Mon Jul 28 03:11:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejf_28180/07_2025/8ejf_28180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejf_28180/07_2025/8ejf_28180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejf_28180/07_2025/8ejf_28180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejf_28180/07_2025/8ejf_28180.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejf_28180/07_2025/8ejf_28180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejf_28180/07_2025/8ejf_28180.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 6081 2.51 5 N 1530 2.21 5 O 2100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9801 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1560 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "a" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1321 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1560 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "b" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1321 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain: "C" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1560 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "c" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1321 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.65, per 1000 atoms: 0.68 Number of scatterers: 9801 At special positions: 0 Unit cell: (94.05, 91.96, 107.635, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2100 8.00 N 1530 7.00 C 6081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=1.80 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.02 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=1.80 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.02 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=1.80 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.02 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 4 " " BMA T 3 " - " MAN T 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " " BMA O 3 " - " MAN O 5 " " BMA R 3 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA W 3 " - " MAN W 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 3 " " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG A 501 " - " ASN A 99 " " NAG B 501 " - " ASN B 99 " " NAG C 501 " - " ASN C 99 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 109 " " NAG G 1 " - " ASN A 119 " " NAG H 1 " - " ASN A 167 " " NAG I 1 " - " ASN A 224 " " NAG J 1 " - " ASN a 365 " " NAG K 1 " - " ASN a 373 " " NAG L 1 " - " ASN B 79 " " NAG M 1 " - " ASN B 89 " " NAG N 1 " - " ASN B 109 " " NAG O 1 " - " ASN B 119 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN B 224 " " NAG R 1 " - " ASN b 365 " " NAG S 1 " - " ASN b 373 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 89 " " NAG V 1 " - " ASN C 109 " " NAG W 1 " - " ASN C 119 " " NAG X 1 " - " ASN C 167 " " NAG Y 1 " - " ASN C 224 " " NAG Z 1 " - " ASN c 365 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " " NAG d 1 " - " ASN c 373 " Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 974.8 milliseconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 36.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.647A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.184A pdb=" N ILE A 201 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'a' and resid 295 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 327 Processing helix chain 'a' and resid 333 through 345 removed outlier: 3.611A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 Processing helix chain 'a' and resid 395 through 400 Processing helix chain 'a' and resid 400 through 417 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.647A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 4.183A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'b' and resid 295 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 327 Processing helix chain 'b' and resid 333 through 345 removed outlier: 3.611A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 Processing helix chain 'b' and resid 395 through 400 Processing helix chain 'b' and resid 400 through 417 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.647A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 4.184A pdb=" N ILE C 201 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'c' and resid 295 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 327 Processing helix chain 'c' and resid 333 through 345 removed outlier: 3.611A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 Processing helix chain 'c' and resid 395 through 400 Processing helix chain 'c' and resid 400 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.758A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 154 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 277 through 280 Processing sheet with id=AA4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.758A pdb=" N HIS B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 154 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 277 through 280 Processing sheet with id=AA8, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 84 through 89 removed outlier: 6.758A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 154 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 277 through 280 Processing sheet with id=AB3, first strand: chain 'c' and resid 388 through 389 333 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1848 1.32 - 1.46: 3260 1.46 - 1.59: 4724 1.59 - 1.73: 32 1.73 - 1.87: 129 Bond restraints: 9993 Sorted by residual: bond pdb=" NE ARG b 422 " pdb=" CZ ARG b 422 " ideal model delta sigma weight residual 1.326 1.407 -0.081 1.10e-02 8.26e+03 5.41e+01 bond pdb=" NE ARG c 422 " pdb=" CZ ARG c 422 " ideal model delta sigma weight residual 1.326 1.407 -0.081 1.10e-02 8.26e+03 5.40e+01 bond pdb=" NE ARG a 422 " pdb=" CZ ARG a 422 " ideal model delta sigma weight residual 1.326 1.407 -0.081 1.10e-02 8.26e+03 5.39e+01 bond pdb=" CB PHE a 399 " pdb=" CG PHE a 399 " ideal model delta sigma weight residual 1.502 1.373 0.129 2.30e-02 1.89e+03 3.17e+01 bond pdb=" CB PHE c 399 " pdb=" CG PHE c 399 " ideal model delta sigma weight residual 1.502 1.373 0.129 2.30e-02 1.89e+03 3.16e+01 ... (remaining 9988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 11867 2.90 - 5.81: 1434 5.81 - 8.71: 208 8.71 - 11.61: 24 11.61 - 14.52: 3 Bond angle restraints: 13536 Sorted by residual: angle pdb=" N ILE b 345 " pdb=" CA ILE b 345 " pdb=" C ILE b 345 " ideal model delta sigma weight residual 112.29 123.82 -11.53 9.40e-01 1.13e+00 1.50e+02 angle pdb=" N ILE c 345 " pdb=" CA ILE c 345 " pdb=" C ILE c 345 " ideal model delta sigma weight residual 112.29 123.80 -11.51 9.40e-01 1.13e+00 1.50e+02 angle pdb=" N ILE a 345 " pdb=" CA ILE a 345 " pdb=" C ILE a 345 " ideal model delta sigma weight residual 112.29 123.80 -11.51 9.40e-01 1.13e+00 1.50e+02 angle pdb=" N SER A 171 " pdb=" CA SER A 171 " pdb=" C SER A 171 " ideal model delta sigma weight residual 114.31 99.79 14.52 1.29e+00 6.01e-01 1.27e+02 angle pdb=" N SER B 171 " pdb=" CA SER B 171 " pdb=" C SER B 171 " ideal model delta sigma weight residual 114.31 99.79 14.52 1.29e+00 6.01e-01 1.27e+02 ... (remaining 13531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 6735 21.24 - 42.49: 216 42.49 - 63.73: 42 63.73 - 84.97: 63 84.97 - 106.21: 66 Dihedral angle restraints: 7122 sinusoidal: 3951 harmonic: 3171 Sorted by residual: dihedral pdb=" CA CYS C 118 " pdb=" CB CYS C 118 " pdb=" SG CYS C 118 " pdb=" SG CYS C 155 " ideal model delta sinusoidal sigma weight residual 79.00 5.99 73.01 1 2.00e+01 2.50e-03 1.70e+01 dihedral pdb=" CA CYS A 118 " pdb=" CB CYS A 118 " pdb=" SG CYS A 118 " pdb=" SG CYS A 155 " ideal model delta sinusoidal sigma weight residual 79.00 6.01 72.99 1 2.00e+01 2.50e-03 1.70e+01 dihedral pdb=" CA CYS B 118 " pdb=" CB CYS B 118 " pdb=" SG CYS B 118 " pdb=" SG CYS B 155 " ideal model delta sinusoidal sigma weight residual 79.00 6.03 72.97 1 2.00e+01 2.50e-03 1.70e+01 ... (remaining 7119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 988 0.106 - 0.212: 421 0.212 - 0.318: 215 0.318 - 0.423: 106 0.423 - 0.529: 25 Chirality restraints: 1755 Sorted by residual: chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 2.62 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 MAN W 4 " pdb=" O3 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 MAN O 4 " pdb=" O3 BMA O 3 " pdb=" C2 MAN O 4 " pdb=" O5 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.13e+02 ... (remaining 1752 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN a 395 " -0.069 2.00e-02 2.50e+03 7.02e-02 6.17e+01 pdb=" CG ASN a 395 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN a 395 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN a 395 " 0.108 2.00e-02 2.50e+03 pdb=" C1 NAG a 702 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN b 395 " 0.068 2.00e-02 2.50e+03 7.02e-02 6.16e+01 pdb=" CG ASN b 395 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN b 395 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN b 395 " -0.108 2.00e-02 2.50e+03 pdb=" C1 NAG b 702 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 395 " -0.068 2.00e-02 2.50e+03 7.01e-02 6.14e+01 pdb=" CG ASN c 395 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN c 395 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN c 395 " 0.107 2.00e-02 2.50e+03 pdb=" C1 NAG c 702 " -0.085 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2691 2.82 - 3.34: 9986 3.34 - 3.86: 16323 3.86 - 4.38: 20471 4.38 - 4.90: 30916 Nonbonded interactions: 80387 Sorted by model distance: nonbonded pdb=" N SER B 171 " pdb=" N TYR B 172 " model vdw 2.299 2.560 nonbonded pdb=" N SER A 171 " pdb=" N TYR A 172 " model vdw 2.299 2.560 nonbonded pdb=" N SER C 171 " pdb=" N TYR C 172 " model vdw 2.300 2.560 nonbonded pdb=" N ASP b 347 " pdb=" OD1 ASP b 347 " model vdw 2.378 3.120 nonbonded pdb=" N ASP c 347 " pdb=" OD1 ASP c 347 " model vdw 2.379 3.120 ... (remaining 80382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.970 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.226 10104 Z= 1.330 Angle : 2.097 15.649 13848 Z= 1.272 Chirality : 0.164 0.529 1755 Planarity : 0.011 0.049 1587 Dihedral : 17.178 106.214 5019 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.23), residues: 1068 helix: -1.24 (0.24), residues: 384 sheet: -0.18 (0.57), residues: 87 loop : -1.38 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.008 TRP B 210 HIS 0.011 0.003 HIS B 93 PHE 0.018 0.006 PHE c 309 TYR 0.088 0.011 TYR C 166 ARG 0.007 0.001 ARG c 314 Details of bonding type rmsd link_NAG-ASN : bond 0.07677 ( 33) link_NAG-ASN : angle 3.91803 ( 99) link_ALPHA1-6 : bond 0.05090 ( 9) link_ALPHA1-6 : angle 2.42488 ( 27) link_BETA1-4 : bond 0.07316 ( 36) link_BETA1-4 : angle 5.29219 ( 108) link_ALPHA1-3 : bond 0.09424 ( 9) link_ALPHA1-3 : angle 7.21873 ( 27) hydrogen bonds : bond 0.17340 ( 333) hydrogen bonds : angle 7.75561 ( 891) link_BETA1-6 : bond 0.08822 ( 3) link_BETA1-6 : angle 7.74284 ( 9) SS BOND : bond 0.08596 ( 21) SS BOND : angle 3.06833 ( 42) covalent geometry : bond 0.02407 ( 9993) covalent geometry : angle 1.99469 (13536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 312 MET cc_start: 0.8327 (mmm) cc_final: 0.8093 (tpp) REVERT: b 359 MET cc_start: 0.8390 (mmm) cc_final: 0.8004 (mmm) REVERT: C 82 MET cc_start: 0.8895 (pmm) cc_final: 0.8468 (pmm) REVERT: c 359 MET cc_start: 0.8275 (mmm) cc_final: 0.7709 (tpp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3307 time to fit residues: 95.1120 Evaluate side-chains 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 0.0030 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 HIS a 406 GLN B 92 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 GLN C 92 HIS ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.055009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.043435 restraints weight = 54549.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.044855 restraints weight = 31134.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045801 restraints weight = 22245.009| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 10104 Z= 0.244 Angle : 1.134 10.898 13848 Z= 0.542 Chirality : 0.051 0.302 1755 Planarity : 0.005 0.034 1587 Dihedral : 16.031 92.760 2988 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.58 % Favored : 89.33 % Rotamer: Outliers : 1.97 % Allowed : 7.04 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.23), residues: 1068 helix: -0.38 (0.26), residues: 381 sheet: -0.12 (0.57), residues: 87 loop : -2.15 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP a 370 HIS 0.007 0.001 HIS a 305 PHE 0.018 0.002 PHE a 309 TYR 0.020 0.002 TYR c 419 ARG 0.006 0.001 ARG a 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00794 ( 33) link_NAG-ASN : angle 3.08734 ( 99) link_ALPHA1-6 : bond 0.00589 ( 9) link_ALPHA1-6 : angle 1.65140 ( 27) link_BETA1-4 : bond 0.01033 ( 36) link_BETA1-4 : angle 3.29399 ( 108) link_ALPHA1-3 : bond 0.00657 ( 9) link_ALPHA1-3 : angle 4.03839 ( 27) hydrogen bonds : bond 0.06308 ( 333) hydrogen bonds : angle 5.98048 ( 891) link_BETA1-6 : bond 0.01873 ( 3) link_BETA1-6 : angle 3.19589 ( 9) SS BOND : bond 0.00975 ( 21) SS BOND : angle 3.82144 ( 42) covalent geometry : bond 0.00551 ( 9993) covalent geometry : angle 1.03395 (13536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7081 (tmt) REVERT: a 359 MET cc_start: 0.8790 (tpp) cc_final: 0.8452 (mtp) REVERT: a 414 MET cc_start: 0.9316 (tmm) cc_final: 0.8843 (tmm) REVERT: B 82 MET cc_start: 0.8992 (pmm) cc_final: 0.8179 (pmm) REVERT: b 414 MET cc_start: 0.9283 (tmm) cc_final: 0.9056 (mtt) REVERT: C 82 MET cc_start: 0.9123 (pmm) cc_final: 0.8468 (pmm) REVERT: C 134 MET cc_start: 0.8771 (tpp) cc_final: 0.8428 (tpp) REVERT: C 194 MET cc_start: 0.9068 (tpt) cc_final: 0.8728 (tpp) REVERT: c 414 MET cc_start: 0.9274 (tmm) cc_final: 0.8743 (tmm) outliers start: 19 outliers final: 11 residues processed: 150 average time/residue: 0.3232 time to fit residues: 66.2516 Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.0060 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.053641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.041895 restraints weight = 56486.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.043304 restraints weight = 32773.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.044236 restraints weight = 23632.866| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10104 Z= 0.210 Angle : 0.974 10.178 13848 Z= 0.466 Chirality : 0.050 0.328 1755 Planarity : 0.004 0.029 1587 Dihedral : 13.454 85.417 2988 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.17 % Favored : 87.73 % Rotamer: Outliers : 2.38 % Allowed : 8.39 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.24), residues: 1068 helix: -0.16 (0.28), residues: 378 sheet: -0.50 (0.58), residues: 87 loop : -2.20 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 210 HIS 0.008 0.001 HIS B 131 PHE 0.014 0.002 PHE c 309 TYR 0.018 0.002 TYR C 150 ARG 0.010 0.001 ARG a 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 33) link_NAG-ASN : angle 2.35115 ( 99) link_ALPHA1-6 : bond 0.00607 ( 9) link_ALPHA1-6 : angle 1.89582 ( 27) link_BETA1-4 : bond 0.00730 ( 36) link_BETA1-4 : angle 2.54244 ( 108) link_ALPHA1-3 : bond 0.00802 ( 9) link_ALPHA1-3 : angle 3.63332 ( 27) hydrogen bonds : bond 0.05063 ( 333) hydrogen bonds : angle 5.79561 ( 891) link_BETA1-6 : bond 0.00594 ( 3) link_BETA1-6 : angle 3.30697 ( 9) SS BOND : bond 0.00857 ( 21) SS BOND : angle 3.50616 ( 42) covalent geometry : bond 0.00463 ( 9993) covalent geometry : angle 0.89454 (13536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8969 (pmm) cc_final: 0.8355 (pmm) REVERT: A 134 MET cc_start: 0.7804 (ttp) cc_final: 0.7415 (tmm) REVERT: B 82 MET cc_start: 0.8722 (pmm) cc_final: 0.8347 (pmm) REVERT: b 410 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7632 (ttm) REVERT: b 414 MET cc_start: 0.9318 (tmm) cc_final: 0.8783 (tmm) REVERT: C 82 MET cc_start: 0.9112 (pmm) cc_final: 0.8396 (pmm) REVERT: C 134 MET cc_start: 0.8700 (tpp) cc_final: 0.8401 (ttm) REVERT: C 194 MET cc_start: 0.9054 (tpt) cc_final: 0.8621 (tpp) REVERT: c 359 MET cc_start: 0.8389 (mmm) cc_final: 0.7928 (mtp) REVERT: c 414 MET cc_start: 0.9367 (tmm) cc_final: 0.8782 (tmm) REVERT: c 417 LYS cc_start: 0.9209 (tppt) cc_final: 0.8933 (ttmm) outliers start: 23 outliers final: 17 residues processed: 135 average time/residue: 0.2450 time to fit residues: 45.7423 Evaluate side-chains 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 26 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.053182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.041495 restraints weight = 56347.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.042879 restraints weight = 32906.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.043826 restraints weight = 23875.617| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10104 Z= 0.179 Angle : 0.875 8.584 13848 Z= 0.416 Chirality : 0.048 0.338 1755 Planarity : 0.004 0.031 1587 Dihedral : 11.977 80.838 2988 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.55 % Favored : 87.17 % Rotamer: Outliers : 2.69 % Allowed : 9.63 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.24), residues: 1068 helix: -0.37 (0.27), residues: 396 sheet: -0.65 (0.57), residues: 87 loop : -2.30 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP c 370 HIS 0.004 0.001 HIS B 124 PHE 0.012 0.001 PHE b 309 TYR 0.015 0.002 TYR b 419 ARG 0.006 0.001 ARG a 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 33) link_NAG-ASN : angle 1.97047 ( 99) link_ALPHA1-6 : bond 0.00570 ( 9) link_ALPHA1-6 : angle 1.91385 ( 27) link_BETA1-4 : bond 0.00606 ( 36) link_BETA1-4 : angle 2.30821 ( 108) link_ALPHA1-3 : bond 0.00758 ( 9) link_ALPHA1-3 : angle 3.69694 ( 27) hydrogen bonds : bond 0.04654 ( 333) hydrogen bonds : angle 5.59842 ( 891) link_BETA1-6 : bond 0.00039 ( 3) link_BETA1-6 : angle 1.28539 ( 9) SS BOND : bond 0.00582 ( 21) SS BOND : angle 2.49881 ( 42) covalent geometry : bond 0.00401 ( 9993) covalent geometry : angle 0.81104 (13536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8877 (pmm) cc_final: 0.8233 (pmm) REVERT: A 134 MET cc_start: 0.7894 (ttp) cc_final: 0.7449 (tmm) REVERT: a 359 MET cc_start: 0.9065 (tpp) cc_final: 0.8747 (mtp) REVERT: a 414 MET cc_start: 0.9312 (tmm) cc_final: 0.8764 (tmm) REVERT: B 134 MET cc_start: 0.9055 (tpp) cc_final: 0.8351 (ttm) REVERT: B 192 MET cc_start: 0.8024 (mpp) cc_final: 0.7819 (mpp) REVERT: b 414 MET cc_start: 0.9345 (tmm) cc_final: 0.8847 (tmm) REVERT: C 82 MET cc_start: 0.9035 (pmm) cc_final: 0.8267 (pmm) REVERT: C 194 MET cc_start: 0.9032 (tpt) cc_final: 0.8478 (tpp) REVERT: c 359 MET cc_start: 0.8544 (mmm) cc_final: 0.8215 (mtp) REVERT: c 414 MET cc_start: 0.9366 (tmm) cc_final: 0.8919 (tmm) outliers start: 26 outliers final: 14 residues processed: 129 average time/residue: 0.2266 time to fit residues: 41.2810 Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 20 optimal weight: 0.0570 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.052731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.041111 restraints weight = 56470.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.042463 restraints weight = 33090.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.043398 restraints weight = 24064.473| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10104 Z= 0.186 Angle : 0.897 10.966 13848 Z= 0.425 Chirality : 0.050 0.339 1755 Planarity : 0.004 0.031 1587 Dihedral : 11.276 77.826 2988 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.64 % Favored : 86.89 % Rotamer: Outliers : 2.48 % Allowed : 11.90 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.24), residues: 1068 helix: -0.69 (0.26), residues: 423 sheet: -0.85 (0.58), residues: 87 loop : -2.57 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 210 HIS 0.016 0.001 HIS C 124 PHE 0.012 0.001 PHE b 309 TYR 0.014 0.002 TYR b 419 ARG 0.004 0.001 ARG a 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 33) link_NAG-ASN : angle 1.99287 ( 99) link_ALPHA1-6 : bond 0.00584 ( 9) link_ALPHA1-6 : angle 1.91148 ( 27) link_BETA1-4 : bond 0.00558 ( 36) link_BETA1-4 : angle 2.18949 ( 108) link_ALPHA1-3 : bond 0.00788 ( 9) link_ALPHA1-3 : angle 3.63257 ( 27) hydrogen bonds : bond 0.04576 ( 333) hydrogen bonds : angle 5.51374 ( 891) link_BETA1-6 : bond 0.00030 ( 3) link_BETA1-6 : angle 1.76478 ( 9) SS BOND : bond 0.01061 ( 21) SS BOND : angle 2.22170 ( 42) covalent geometry : bond 0.00408 ( 9993) covalent geometry : angle 0.83936 (13536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8877 (pmm) cc_final: 0.8328 (pmm) REVERT: A 134 MET cc_start: 0.8073 (ttp) cc_final: 0.7612 (tmm) REVERT: A 194 MET cc_start: 0.9204 (tpt) cc_final: 0.8792 (tpp) REVERT: a 414 MET cc_start: 0.9330 (tmm) cc_final: 0.8858 (tmm) REVERT: B 82 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7746 (pmm) REVERT: B 134 MET cc_start: 0.8952 (tpp) cc_final: 0.8327 (ttm) REVERT: B 203 LEU cc_start: 0.7665 (mt) cc_final: 0.7365 (tt) REVERT: b 308 GLU cc_start: 0.9169 (mp0) cc_final: 0.8563 (mt-10) REVERT: b 414 MET cc_start: 0.9374 (tmm) cc_final: 0.8933 (tmm) REVERT: C 82 MET cc_start: 0.8997 (pmm) cc_final: 0.8390 (pmm) REVERT: C 194 MET cc_start: 0.9069 (tpt) cc_final: 0.8698 (tpp) REVERT: C 210 TRP cc_start: 0.6276 (t-100) cc_final: 0.5837 (t-100) REVERT: c 351 MET cc_start: 0.9326 (mmm) cc_final: 0.8791 (mmm) REVERT: c 359 MET cc_start: 0.8549 (mmm) cc_final: 0.8345 (mtp) REVERT: c 414 MET cc_start: 0.9391 (tmm) cc_final: 0.8844 (tmm) REVERT: c 417 LYS cc_start: 0.9261 (tppt) cc_final: 0.8904 (ttmm) outliers start: 24 outliers final: 18 residues processed: 128 average time/residue: 0.2203 time to fit residues: 39.6779 Evaluate side-chains 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 90 ASN b 354 HIS C 90 ASN ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.051428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.039695 restraints weight = 57495.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.041001 restraints weight = 34675.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041889 restraints weight = 25437.976| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10104 Z= 0.257 Angle : 0.924 8.413 13848 Z= 0.436 Chirality : 0.050 0.333 1755 Planarity : 0.004 0.029 1587 Dihedral : 10.968 76.203 2988 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.83 % Favored : 86.61 % Rotamer: Outliers : 2.80 % Allowed : 12.73 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.24), residues: 1068 helix: -0.79 (0.26), residues: 420 sheet: 0.72 (0.58), residues: 75 loop : -2.77 (0.22), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 210 HIS 0.005 0.001 HIS a 305 PHE 0.014 0.002 PHE a 309 TYR 0.015 0.002 TYR B 241 ARG 0.004 0.001 ARG B 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 33) link_NAG-ASN : angle 2.13420 ( 99) link_ALPHA1-6 : bond 0.00565 ( 9) link_ALPHA1-6 : angle 1.90793 ( 27) link_BETA1-4 : bond 0.00545 ( 36) link_BETA1-4 : angle 2.17174 ( 108) link_ALPHA1-3 : bond 0.00812 ( 9) link_ALPHA1-3 : angle 3.49334 ( 27) hydrogen bonds : bond 0.04794 ( 333) hydrogen bonds : angle 5.61093 ( 891) link_BETA1-6 : bond 0.00328 ( 3) link_BETA1-6 : angle 2.25383 ( 9) SS BOND : bond 0.00790 ( 21) SS BOND : angle 2.14586 ( 42) covalent geometry : bond 0.00558 ( 9993) covalent geometry : angle 0.86799 (13536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8947 (pmm) cc_final: 0.8436 (pmm) REVERT: A 134 MET cc_start: 0.8266 (ttp) cc_final: 0.7840 (tmm) REVERT: A 194 MET cc_start: 0.9244 (tpt) cc_final: 0.8798 (tpp) REVERT: a 300 LYS cc_start: 0.9479 (mttt) cc_final: 0.9230 (mttt) REVERT: a 320 LYS cc_start: 0.9497 (tptp) cc_final: 0.9097 (tptp) REVERT: a 359 MET cc_start: 0.9176 (tpp) cc_final: 0.8821 (mmm) REVERT: a 414 MET cc_start: 0.9381 (tmm) cc_final: 0.8983 (tmm) REVERT: B 82 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7956 (pmm) REVERT: B 203 LEU cc_start: 0.7661 (mt) cc_final: 0.7307 (tt) REVERT: b 414 MET cc_start: 0.9376 (tmm) cc_final: 0.8950 (tmm) REVERT: C 82 MET cc_start: 0.9037 (pmm) cc_final: 0.8833 (pmm) REVERT: C 134 MET cc_start: 0.8167 (ttm) cc_final: 0.7471 (tmm) REVERT: C 194 MET cc_start: 0.9210 (tpt) cc_final: 0.8823 (tpp) REVERT: C 210 TRP cc_start: 0.6531 (t-100) cc_final: 0.6032 (t-100) REVERT: c 414 MET cc_start: 0.9401 (tmm) cc_final: 0.8864 (tmm) outliers start: 27 outliers final: 21 residues processed: 120 average time/residue: 0.2166 time to fit residues: 37.4422 Evaluate side-chains 119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.052493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.040661 restraints weight = 56539.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.041973 restraints weight = 33948.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.042875 restraints weight = 24896.642| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10104 Z= 0.178 Angle : 0.879 10.477 13848 Z= 0.410 Chirality : 0.050 0.356 1755 Planarity : 0.004 0.044 1587 Dihedral : 10.314 72.918 2988 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.73 % Favored : 86.70 % Rotamer: Outliers : 2.17 % Allowed : 15.01 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.24), residues: 1068 helix: -0.49 (0.27), residues: 393 sheet: 0.54 (0.56), residues: 75 loop : -2.62 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 210 HIS 0.004 0.001 HIS a 305 PHE 0.014 0.001 PHE b 309 TYR 0.013 0.001 TYR c 366 ARG 0.004 0.001 ARG a 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 33) link_NAG-ASN : angle 1.96235 ( 99) link_ALPHA1-6 : bond 0.00602 ( 9) link_ALPHA1-6 : angle 1.88022 ( 27) link_BETA1-4 : bond 0.00528 ( 36) link_BETA1-4 : angle 2.09115 ( 108) link_ALPHA1-3 : bond 0.00707 ( 9) link_ALPHA1-3 : angle 3.67888 ( 27) hydrogen bonds : bond 0.04453 ( 333) hydrogen bonds : angle 5.44813 ( 891) link_BETA1-6 : bond 0.00038 ( 3) link_BETA1-6 : angle 1.94407 ( 9) SS BOND : bond 0.00888 ( 21) SS BOND : angle 2.02227 ( 42) covalent geometry : bond 0.00393 ( 9993) covalent geometry : angle 0.82300 (13536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8241 (ttp) cc_final: 0.7799 (tmm) REVERT: a 320 LYS cc_start: 0.9490 (tptp) cc_final: 0.9115 (tptp) REVERT: B 82 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7843 (pmm) REVERT: B 134 MET cc_start: 0.9024 (tpp) cc_final: 0.8766 (tpp) REVERT: B 203 LEU cc_start: 0.7565 (mt) cc_final: 0.7293 (tt) REVERT: b 414 MET cc_start: 0.9394 (tmm) cc_final: 0.9034 (tmm) REVERT: C 82 MET cc_start: 0.8982 (pmm) cc_final: 0.8766 (pmm) REVERT: C 134 MET cc_start: 0.8331 (ttm) cc_final: 0.7639 (tmm) REVERT: C 194 MET cc_start: 0.9167 (tpt) cc_final: 0.8780 (tpp) REVERT: C 210 TRP cc_start: 0.6335 (t-100) cc_final: 0.5961 (t-100) REVERT: c 311 ASP cc_start: 0.9221 (m-30) cc_final: 0.8609 (m-30) REVERT: c 351 MET cc_start: 0.9266 (mmm) cc_final: 0.8734 (mmm) REVERT: c 414 MET cc_start: 0.9401 (tmm) cc_final: 0.8875 (tmm) outliers start: 21 outliers final: 18 residues processed: 126 average time/residue: 0.2603 time to fit residues: 45.8171 Evaluate side-chains 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 9 optimal weight: 0.0370 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.053250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.041476 restraints weight = 56371.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.042816 restraints weight = 33547.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.043743 restraints weight = 24407.540| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10104 Z= 0.155 Angle : 0.866 10.938 13848 Z= 0.407 Chirality : 0.049 0.354 1755 Planarity : 0.004 0.040 1587 Dihedral : 9.787 69.970 2988 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.48 % Favored : 85.96 % Rotamer: Outliers : 1.45 % Allowed : 16.05 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.24), residues: 1068 helix: -0.16 (0.27), residues: 381 sheet: 0.39 (0.63), residues: 57 loop : -2.56 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 210 HIS 0.008 0.001 HIS c 305 PHE 0.012 0.001 PHE b 309 TYR 0.012 0.001 TYR c 366 ARG 0.016 0.001 ARG b 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 33) link_NAG-ASN : angle 1.85982 ( 99) link_ALPHA1-6 : bond 0.00635 ( 9) link_ALPHA1-6 : angle 1.81063 ( 27) link_BETA1-4 : bond 0.00535 ( 36) link_BETA1-4 : angle 2.07764 ( 108) link_ALPHA1-3 : bond 0.00664 ( 9) link_ALPHA1-3 : angle 3.59201 ( 27) hydrogen bonds : bond 0.04292 ( 333) hydrogen bonds : angle 5.40060 ( 891) link_BETA1-6 : bond 0.00157 ( 3) link_BETA1-6 : angle 1.78670 ( 9) SS BOND : bond 0.00641 ( 21) SS BOND : angle 1.82979 ( 42) covalent geometry : bond 0.00342 ( 9993) covalent geometry : angle 0.81446 (13536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8258 (ttp) cc_final: 0.7963 (tmm) REVERT: A 192 MET cc_start: 0.8093 (mpp) cc_final: 0.7823 (mpp) REVERT: a 311 ASP cc_start: 0.9170 (m-30) cc_final: 0.8755 (m-30) REVERT: a 414 MET cc_start: 0.9272 (tmm) cc_final: 0.8759 (tmm) REVERT: B 82 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7670 (pmm) REVERT: B 134 MET cc_start: 0.8990 (tpp) cc_final: 0.8746 (tpp) REVERT: B 203 LEU cc_start: 0.7571 (mt) cc_final: 0.7370 (tt) REVERT: b 332 MET cc_start: 0.8910 (tpp) cc_final: 0.8530 (tpp) REVERT: b 414 MET cc_start: 0.9396 (tmm) cc_final: 0.8884 (tmm) REVERT: C 82 MET cc_start: 0.8933 (pmm) cc_final: 0.8379 (pmm) REVERT: C 134 MET cc_start: 0.8398 (ttm) cc_final: 0.7702 (tmm) REVERT: C 153 MET cc_start: 0.6539 (mpp) cc_final: 0.6336 (mpp) REVERT: C 194 MET cc_start: 0.9065 (tpt) cc_final: 0.8674 (tpp) REVERT: c 303 GLU cc_start: 0.8875 (pm20) cc_final: 0.8433 (tp30) REVERT: c 311 ASP cc_start: 0.9164 (m-30) cc_final: 0.8551 (m-30) REVERT: c 414 MET cc_start: 0.9471 (tmm) cc_final: 0.8949 (tmm) outliers start: 14 outliers final: 12 residues processed: 118 average time/residue: 0.2020 time to fit residues: 34.6021 Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.053739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.041937 restraints weight = 56869.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.043299 restraints weight = 33961.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.044255 restraints weight = 24601.790| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10104 Z= 0.152 Angle : 0.858 10.042 13848 Z= 0.403 Chirality : 0.048 0.352 1755 Planarity : 0.004 0.043 1587 Dihedral : 9.456 67.592 2988 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.75 % Allowed : 12.92 % Favored : 86.33 % Rotamer: Outliers : 1.86 % Allowed : 16.15 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.24), residues: 1068 helix: -0.20 (0.27), residues: 390 sheet: 0.29 (0.63), residues: 57 loop : -2.50 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 210 HIS 0.004 0.001 HIS c 305 PHE 0.008 0.001 PHE C 233 TYR 0.011 0.001 TYR c 366 ARG 0.015 0.001 ARG c 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 33) link_NAG-ASN : angle 1.81797 ( 99) link_ALPHA1-6 : bond 0.00646 ( 9) link_ALPHA1-6 : angle 1.76728 ( 27) link_BETA1-4 : bond 0.00524 ( 36) link_BETA1-4 : angle 2.06142 ( 108) link_ALPHA1-3 : bond 0.00632 ( 9) link_ALPHA1-3 : angle 3.51871 ( 27) hydrogen bonds : bond 0.04054 ( 333) hydrogen bonds : angle 5.34305 ( 891) link_BETA1-6 : bond 0.00218 ( 3) link_BETA1-6 : angle 1.73302 ( 9) SS BOND : bond 0.00601 ( 21) SS BOND : angle 1.75813 ( 42) covalent geometry : bond 0.00340 ( 9993) covalent geometry : angle 0.80815 (13536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8299 (ttp) cc_final: 0.7907 (tmm) REVERT: a 311 ASP cc_start: 0.9153 (m-30) cc_final: 0.8746 (m-30) REVERT: a 414 MET cc_start: 0.9287 (tmm) cc_final: 0.8767 (tmm) REVERT: B 82 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7642 (pmm) REVERT: B 134 MET cc_start: 0.8945 (tpp) cc_final: 0.8628 (tpp) REVERT: B 153 MET cc_start: 0.6239 (mpp) cc_final: 0.5867 (mpp) REVERT: b 311 ASP cc_start: 0.9261 (m-30) cc_final: 0.8479 (m-30) REVERT: b 332 MET cc_start: 0.8986 (tpp) cc_final: 0.8600 (tpp) REVERT: b 414 MET cc_start: 0.9407 (tmm) cc_final: 0.8961 (tmm) REVERT: C 82 MET cc_start: 0.8900 (pmm) cc_final: 0.8313 (pmm) REVERT: C 134 MET cc_start: 0.8198 (ttm) cc_final: 0.7361 (tmm) REVERT: C 153 MET cc_start: 0.6475 (mpp) cc_final: 0.6264 (mpp) REVERT: C 194 MET cc_start: 0.9039 (tpt) cc_final: 0.8640 (tpp) REVERT: c 311 ASP cc_start: 0.9155 (m-30) cc_final: 0.8601 (m-30) REVERT: c 414 MET cc_start: 0.9444 (tmm) cc_final: 0.8981 (tmm) outliers start: 18 outliers final: 12 residues processed: 117 average time/residue: 0.2563 time to fit residues: 44.3814 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.052523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.040860 restraints weight = 57310.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.042191 restraints weight = 34217.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.043109 restraints weight = 24845.604| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10104 Z= 0.200 Angle : 0.896 10.418 13848 Z= 0.422 Chirality : 0.049 0.337 1755 Planarity : 0.004 0.038 1587 Dihedral : 9.521 66.721 2988 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.84 % Allowed : 12.36 % Favored : 86.80 % Rotamer: Outliers : 1.45 % Allowed : 16.77 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.25), residues: 1068 helix: -0.38 (0.27), residues: 408 sheet: 0.35 (0.57), residues: 75 loop : -2.60 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 210 HIS 0.004 0.001 HIS a 305 PHE 0.036 0.002 PHE C 147 TYR 0.016 0.002 TYR B 217 ARG 0.013 0.001 ARG c 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 33) link_NAG-ASN : angle 1.92151 ( 99) link_ALPHA1-6 : bond 0.00585 ( 9) link_ALPHA1-6 : angle 1.73170 ( 27) link_BETA1-4 : bond 0.00505 ( 36) link_BETA1-4 : angle 2.06796 ( 108) link_ALPHA1-3 : bond 0.00640 ( 9) link_ALPHA1-3 : angle 3.29918 ( 27) hydrogen bonds : bond 0.04181 ( 333) hydrogen bonds : angle 5.47332 ( 891) link_BETA1-6 : bond 0.00142 ( 3) link_BETA1-6 : angle 2.09578 ( 9) SS BOND : bond 0.00694 ( 21) SS BOND : angle 1.82838 ( 42) covalent geometry : bond 0.00448 ( 9993) covalent geometry : angle 0.84826 (13536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8352 (ttp) cc_final: 0.8013 (tmm) REVERT: a 311 ASP cc_start: 0.9158 (m-30) cc_final: 0.8744 (m-30) REVERT: a 332 MET cc_start: 0.8916 (tpt) cc_final: 0.8628 (tpt) REVERT: a 414 MET cc_start: 0.9277 (tmm) cc_final: 0.8780 (tmm) REVERT: B 82 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7492 (pmm) REVERT: B 134 MET cc_start: 0.8963 (tpp) cc_final: 0.8582 (tpp) REVERT: B 153 MET cc_start: 0.6498 (mpp) cc_final: 0.6165 (mpp) REVERT: b 311 ASP cc_start: 0.9287 (m-30) cc_final: 0.8507 (m-30) REVERT: b 332 MET cc_start: 0.8962 (tpp) cc_final: 0.8554 (tpp) REVERT: b 399 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8425 (t80) REVERT: b 414 MET cc_start: 0.9392 (tmm) cc_final: 0.8907 (tmm) REVERT: C 82 MET cc_start: 0.9038 (pmm) cc_final: 0.8815 (pmm) REVERT: C 134 MET cc_start: 0.8200 (ttm) cc_final: 0.7343 (tmm) REVERT: C 194 MET cc_start: 0.9144 (tpt) cc_final: 0.8780 (tpp) REVERT: c 311 ASP cc_start: 0.9152 (m-30) cc_final: 0.8577 (m-30) REVERT: c 333 SER cc_start: 0.8520 (m) cc_final: 0.7961 (p) REVERT: c 414 MET cc_start: 0.9443 (tmm) cc_final: 0.8991 (tmm) REVERT: c 417 LYS cc_start: 0.9179 (tppt) cc_final: 0.8955 (ttmm) outliers start: 14 outliers final: 12 residues processed: 104 average time/residue: 0.2433 time to fit residues: 37.5804 Evaluate side-chains 104 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 399 PHE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 0.0050 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.053105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.041753 restraints weight = 56398.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.043141 restraints weight = 32342.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.044094 restraints weight = 22962.375| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10104 Z= 0.160 Angle : 0.874 11.326 13848 Z= 0.411 Chirality : 0.048 0.352 1755 Planarity : 0.004 0.035 1587 Dihedral : 9.244 64.101 2988 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.84 % Allowed : 12.27 % Favored : 86.89 % Rotamer: Outliers : 1.45 % Allowed : 16.67 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.25), residues: 1068 helix: -0.12 (0.27), residues: 390 sheet: 0.29 (0.58), residues: 75 loop : -2.59 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP B 210 HIS 0.004 0.001 HIS C 124 PHE 0.034 0.001 PHE C 147 TYR 0.017 0.001 TYR b 371 ARG 0.012 0.001 ARG c 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 33) link_NAG-ASN : angle 1.82951 ( 99) link_ALPHA1-6 : bond 0.00635 ( 9) link_ALPHA1-6 : angle 1.69867 ( 27) link_BETA1-4 : bond 0.00507 ( 36) link_BETA1-4 : angle 2.04305 ( 108) link_ALPHA1-3 : bond 0.00594 ( 9) link_ALPHA1-3 : angle 3.43423 ( 27) hydrogen bonds : bond 0.04140 ( 333) hydrogen bonds : angle 5.42707 ( 891) link_BETA1-6 : bond 0.00064 ( 3) link_BETA1-6 : angle 1.85306 ( 9) SS BOND : bond 0.00625 ( 21) SS BOND : angle 1.82779 ( 42) covalent geometry : bond 0.00363 ( 9993) covalent geometry : angle 0.82623 (13536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2987.40 seconds wall clock time: 55 minutes 43.11 seconds (3343.11 seconds total)